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angsd of different build retain no sites #405

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sagitaninta opened this issue Jun 29, 2021 · 2 comments · Fixed by #533
Closed

angsd of different build retain no sites #405

sagitaninta opened this issue Jun 29, 2021 · 2 comments · Fixed by #533

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@sagitaninta
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sagitaninta commented Jun 29, 2021 •
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I have been using angsd version: 0.933-79-gda26ba4 (htslib: 1.10.2) build(Jun 24 2020 10:30:09) with the following command to get genotype likelihood of selected sites and it has been going well in our server, say server A:

angsd -i input/${file} -sites sites.file -r autosomes -out glf_files/${file%.bam} -minQ 20 -minMapQ 20 -remove_bads 1 -trim 5 -GL 2 -doGlf 4

This is the result

	-> angsd version: 0.933-79-gda26ba4 (htslib: 1.10.2) build(Jun 24 2020 10:30:09)
	-> /home/btx638/software/angsd/angsd -i RD42_mdup.bam -sites chr10_sift.file -r 10 -out test_chr10 -minQ 20 -minMapQ 20 -remove_bads 1 -trim 5 -GL 2 -doGlf 4 
        -> Inputtype is BAM/CRAM
[multiReader] 1 samples in 1 input files
	-> [prep_sites.cpp] Reading binary representation of 'chr10_sift.file'
	-> [prep_sites.cpp] nChr: 1 loaded from binary filter file
	-> [abcFilter.cpp] -sites is still beta, use at own risk...
	-> Parsing 1 number of samples 
	-> Region lookup 1/1
	-> Printing at chr: 10 pos:69315074 chunknumber 90600 contains 813 sitess
	-> Done reading data waiting for calculations to finish
	-> Done waiting for threads
	-> Output filenames:
		->"test_chr10.arg"
		->"test_chr10.glf.gz"
	-> Mon Jun 28 12:38:17 2021
	-> Arguments and parameters for all analysis are located in .arg file
	-> Total number of sites analyzed: 66406506
	-> Number of sites retained after filtering: 269913 
	[ALL done] cpu-time used = 56.72 sec
	[ALL done] walltime used = 56.00 sec

But the exact same command with same sites, same BAM, same angsd and htslib version, different server, say server B, just installed from conda instead from github like what I did in server A, do not retain any sites:

angsd -i RD42_mdup.bam -sites chr10_100s.file -r 10 -out test_chr10 -remove_bads 1 -minQ 20 -minMapQ 20 -trim 5 -GL 2 -doGlf 4
        -> angsd version: 0.933 (htslib: 1.10.2) build(Jun 6 2020 19:47:54)
	-> [prep_sites.cpp] Reading binary representation of 'chr10_100s.file'
	-> [prep_sites.cpp] nChr: 1 loaded from binary filter file
	-> [abcFilter.cpp] -sites is still beta, use at own risk...
[bammer_main] 1 samples in 1 input files
	-> Parsing 1 number of samples 
	-> Region lookup 1/1
	-> Printing at chr: 10 pos:69297562 chunknumber 89400 contains 832 sitess
	-> Done reading data waiting for calculations to finish
	-> Done waiting for threads
	-> Output filenames:
		->"test_chr10.arg"
		->"test_chr10.glf.gz"
	-> Mon Jun 28 14:12:46 2021
	-> Arguments and parameters for all analysis are located in .arg file
	-> Total number of sites analyzed: 66380991
	-> Number of sites retained after filtering: 0 
	[ALL done] cpu-time used = 59.61 sec
	[ALL done] walltime used = 60.00 sec

I actually also noticed that the same version of angsd analysed different number of sites of the same BAM file even when I specify the same chromosome using -r. Could someone point me how to fix this? I have also compiled the newest version of ANGSD from github in my home directory in the server B. I have checked also if the sites actually exist; it output GL in using the same version of ANGSD in server A so it should be there.
@tholtzem
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tholtzem commented Jul 8, 2021

Similar issue : Sites are not retained using "-sites" option using angsd 0.935

I have been using angsd version: 0.935 (htslib: 1.12) build (Mar 28 2021 01:00:43) installed from conda using the command shown below. Unfortunately, the sites are not retained in the output files (see output for beagle.gz, mafs.gz).

BUT when I use the angsd version: 0.921 (htslib: 1.9) build (Aug 6 2018 13:54:50) installed from conda using the same command sites are retained as expected.

I also tested the angsd version: 0.921 (htslib: 1.6) build (Jun 3 2019 10:11:40) installed from github, which works fine as well. So in my case, the issue seems to be the version and not the installation via conda

My commands:

# index SNP list
angsd sites index list/LDpruned_snps_chrom1.list

# Calculate genotype likelihoods on predefined sites using angsd
angsd -b 'list/realignedBAM_depth10.list' -anc reference.fa -out angsd/angsd_LC_GL2_maf0018_LDpruned_chrom1 -GL 2 -doGlf 2 -doMajorMinor 3 -doMaf 1 -doCounts 1 -sites 'list/LDpruned_snps_chrom1.list' -rf list/LDpruned_Chrom_chrom1.list
  1. beagle output, using angsd version: 0.935 (htslib: 1.12) build (Mar 28 2021 01:00:43)
zcat angsd/angsd_LC_GL2_maf0018_LDpruned_chrom1.beagle.gz | head

marker	allele1	allele2	Ind0	Ind0	Ind0	Ind1	Ind1	Ind1	Ind2	Ind2	Ind2	Ind3	Ind3	Ind3	Ind4	Ind4	Ind4	Ind5	Ind5	Ind5	Ind6	Ind6	Ind6	Ind7	Ind7	Ind7	Ind8	Ind8	Ind8	Ind9	Ind9	Ind9	Ind10	Ind10	Ind10	Ind11	Ind11	Ind11	Ind12	Ind12	Ind12	Ind13	Ind13	Ind13	Ind14	Ind14	Ind14	Ind15	Ind15	Ind15	Ind16	Ind16	Ind16	Ind17	Ind17	Ind17	Ind18	Ind18	Ind18	Ind19	Ind19	Ind19	Ind20	Ind20	Ind20	Ind21	Ind21	Ind21	Ind22	Ind22	Ind22	Ind23	Ind23	Ind23	Ind24	Ind24	Ind24	Ind25	Ind25	Ind25	Ind26	Ind26	Ind26	Ind27	Ind27	Ind27	Ind28	Ind28	Ind28	Ind29	Ind29	Ind29	Ind30	Ind30	Ind30	Ind31	Ind31	Ind31	Ind32	Ind32	Ind32	Ind33	Ind33	Ind33	Ind34	Ind34	Ind34	Ind35	Ind35	Ind35	Ind36	Ind36	Ind36	Ind37	Ind37	Ind37	Ind38	Ind38	Ind38	Ind39	Ind39	Ind39	Ind40	Ind40	Ind40	Ind41	Ind41	Ind41	Ind42	Ind42	Ind42	Ind43	Ind43	Ind43	Ind44	Ind44	Ind44	Ind45	Ind45	Ind45	Ind46	Ind46	Ind46	Ind47	Ind47	Ind47	Ind48	Ind48	Ind48	Ind49	Ind49	Ind49	Ind50	Ind50	Ind50	Ind51	Ind51	Ind51	Ind52	Ind52	Ind52	Ind53	Ind53	Ind53	Ind54	Ind54	Ind54
  1. mafs output, using angsd version: 0.935 (htslib: 1.12) build (Mar 28 2021 01:00:43)
zcat angsd/angsd_LC_GL2_maf0018_LDpruned_chrom1.mafs.gz |  head

chromo	position	major	minor	anc	knownEM	nInd
  1. log output, using angsd version: 0.935 (htslib: 1.12) build (Mar 28 2021 01:00:43)
-> angsd version: 0.935 (htslib: 1.12) build(Mar 28 2021 01:00:43)
	-> angsd -b list/realignedBAM_depth10.list -anc reference.fa -out angsd/angsd_LC_GL2_maf0018_LDpruned_chrom1 -GL 2 -doGlf 2 -doMajorMinor 3 -doMaf 1 -doCounts 1 -sites list/LDpruned_snps_chrom1.list -rf list/LDpruned_Chrom_chrom1.list 
	-> Inputtype is BAM/CRAM
[multiReader] 55 samples in 55 input files
	-> [prep_sites.cpp] Reading binary representation of 'list/LDpruned_snps_chrom1.list'
	-> [prep_sites.cpp] nChr: 1 loaded from binary filter file
	-> Filterfile contains major/minor information
	-> [abcFilter.cpp] -sites is still beta, use at own risk...
	-> Reading fasta: reference.fasta
	-> Parsing 55 number of samples 
	-> Region lookup 1/1

	-> Allocated ~ 10 million nodes to the nodepool, this is not an estimate of the memory usage
	-> Printing at chr: chrom1 pos:26605 chunknumber 100 contains 251 sites
	-> Printing at chr: chrom1 pos:54087 chunknumber 200 contains 536 sites

	-> Allocated ~ 20 million nodes to the nodepool, this is not an estimate of the memory usage
	-> Printing at chr: chrom1 pos:83464 chunknumber 300 contains 251 sites

	-> Allocated ~ 30 million nodes to the nodepool, this is not an estimate of the memory usage

	-> Allocated ~ 40 million nodes to the nodepool, this is not an estimate of the memory usage

	-> Allocated ~ 50 million nodes to the nodepool, this is not an estimate of the memory usage

	-> Allocated ~ 60 million nodes to the nodepool, this is not an estimate of the memory usage

	-> Allocated ~ 70 million nodes to the nodepool, this is not an estimate of the memory usage
	-> Printing at chr: chrom1 pos:125739 chunknumber 400 contains 322 sites
	-> Printing at chr: chrom1 pos:159057 chunknumber 500 contains 261 sites
	-> Printing at chr: chrom1 pos:185071 chunknumber 600 contains 252 sites
	-> Printing at chr: chrom1 pos:210603 chunknumber 700 contains 266 sites
	-> Printing at chr: chrom1 pos:235998 chunknumber 800 contains 252 sites
	-> Printing at chr: chrom1 pos:261687 chunknumber 900 contains 252 sites
	-> Printing at chr: chrom1 pos:287788 chunknumber 1000 contains 255 sites
	-> Printing at chr: chrom1 pos:313237 chunknumber 1100 contains 255 sites
	-> Printing at chr: chrom1 pos:341463 chunknumber 1200 contains 251 sites
	-> Printing at chr: chrom1 pos:367023 chunknumber 1300 contains 265 sites
	-> Printing at chr: chrom1 pos:392993 chunknumber 1400 contains 251 sites
	-> Printing at chr: chrom1 pos:421985 chunknumber 1500 contains 255 sites
	-> Printing at chr: chrom1 pos:447407 chunknumber 1600 contains 251 sites
	-> Printing at chr: chrom1 pos:473372 chunknumber 1700 contains 254 sites
	-> Printing at chr: chrom1 pos:499139 chunknumber 1800 contains 252 sites
	-> Printing at chr: chrom1 pos:524574 chunknumber 1900 contains 272 sites
	-> Printing at chr: chrom1 pos:550791 chunknumber 2000 contains 251 sites
	-> Printing at chr: chrom1 pos:576997 chunknumber 2100 contains 251 sites
	-> Printing at chr: chrom1 pos:602613 chunknumber 2200 contains 256 sites
	-> Printing at chr: chrom1 pos:628188 chunknumber 2300 contains 252 sites
	-> Printing at chr: chrom1 pos:654714 chunknumber 2400 contains 256 sites
	-> Printing at chr: chrom1 pos:680273 chunknumber 2500 contains 252 sites
	-> Printing at chr: chrom1 pos:705826 chunknumber 2600 contains 251 sites
	-> Printing at chr: chrom1 pos:731715 chunknumber 2700 contains 252 sites
	-> Printing at chr: chrom1 pos:757188 chunknumber 2800 contains 255 sites
	-> Printing at chr: chrom1 pos:782836 chunknumber 2900 contains 252 sites
	-> Printing at chr: chrom1 pos:808468 chunknumber 3000 contains 251 sites
	-> Printing at chr: chrom1 pos:835340 chunknumber 3100 contains 256 sites
	-> Printing at chr: chrom1 pos:860744 chunknumber 3200 contains 259 sites
	-> Printing at chr: chrom1 pos:886811 chunknumber 3300 contains 251 sites
	-> Printing at chr: chrom1 pos:912573 chunknumber 3400 contains 259 sites
	-> Printing at chr: chrom1 pos:938142 chunknumber 3500 contains 262 sites
	-> Printing at chr: chrom1 pos:968970 chunknumber 3600 contains 254 sites
	-> Printing at chr: chrom1 pos:997235 chunknumber 3700 contains 441 sites
	-> Printing at chr: chrom1 pos:1024752 chunknumber 3800 contains 252 sites
	-> Printing at chr: chrom1 pos:1052940 chunknumber 3900 contains 252 sites
	-> Printing at chr: chrom1 pos:1091770 chunknumber 4000 contains 251 sites
	-> Printing at chr: chrom1 pos:1117345 chunknumber 4100 contains 256 sites
	-> Printing at chr: chrom1 pos:1143084 chunknumber 4200 contains 252 sites
	-> Printing at chr: chrom1 pos:1168761 chunknumber 4300 contains 252 sites
	-> Printing at chr: chrom1 pos:1194498 chunknumber 4400 contains 253 sites
	-> Printing at chr: chrom1 pos:1219894 chunknumber 4500 contains 254 sites
	-> Printing at chr: chrom1 pos:1245388 chunknumber 4600 contains 253 sites
	-> Printing at chr: chrom1 pos:1270824 chunknumber 4700 contains 251 sites
	-> Printing at chr: chrom1 pos:1296372 chunknumber 4800 contains 252 sites
	-> Printing at chr: chrom1 pos:1321719 chunknumber 4900 contains 253 sites
	-> Printing at chr: chrom1 pos:1347777 chunknumber 5000 contains 251 sites
	-> Printing at chr: chrom1 pos:1373438 chunknumber 5100 contains 256 sites
	-> Printing at chr: chrom1 pos:1398893 chunknumber 5200 contains 253 sites
	-> Printing at chr: chrom1 pos:1433295 chunknumber 5300 contains 266 sites
	-> Printing at chr: chrom1 pos:1461135 chunknumber 5400 contains 252 sites
	-> Printing at chr: chrom1 pos:1488105 chunknumber 5500 contains 251 sites
	-> Printing at chr: chrom1 pos:1513731 chunknumber 5600 contains 254 sites
	-> Printing at chr: chrom1 pos:1539407 chunknumber 5700 contains 255 sites
	-> Printing at chr: chrom1 pos:1565194 chunknumber 5800 contains 253 sites
	-> Printing at chr: chrom1 pos:1591515 chunknumber 5900 contains 252 sites
	-> Printing at chr: chrom1 pos:1617466 chunknumber 6000 contains 264 sites
	-> Printing at chr: chrom1 pos:1642919 chunknumber 6100 contains 252 sites
	-> Printing at chr: chrom1 pos:1668362 chunknumber 6200 contains 255 sites
	-> Printing at chr: chrom1 pos:1697488 chunknumber 6300 contains 360 sites
	-> Printing at chr: chrom1 pos:1725824 chunknumber 6400 contains 252 sites
	-> Printing at chr: chrom1 pos:1751404 chunknumber 6500 contains 256 sites
	-> Printing at chr: chrom1 pos:1776875 chunknumber 6600 contains 285 sites
	-> Printing at chr: chrom1 pos:1822075 chunknumber 6700 contains 286 sites
	-> Printing at chr: chrom1 pos:1847550 chunknumber 6800 contains 253 sites
	-> Printing at chr: chrom1 pos:1875196 chunknumber 6900 contains 254 sites
	-> Printing at chr: chrom1 pos:1902184 chunknumber 7000 contains 514 sites
	-> Printing at chr: chrom1 pos:1947622 chunknumber 7100 contains 373 sites
	-> Printing at chr: chrom1 pos:1976072 chunknumber 7200 contains 252 sites
	-> Printing at chr: chrom1 pos:2002074 chunknumber 7300 contains 256 sites
	-> Printing at chr: chrom1 pos:2035738 chunknumber 7400 contains 254 sites
	-> Printing at chr: chrom1 pos:2063953 chunknumber 7500 contains 255 sites
	-> Printing at chr: chrom1 pos:2089757 chunknumber 7600 contains 251 sites
	-> Printing at chr: chrom1 pos:2115834 chunknumber 7700 contains 253 sites
	-> Printing at chr: chrom1 pos:2141217 chunknumber 7800 contains 251 sites
	-> Printing at chr: chrom1 pos:2167133 chunknumber 7900 contains 258 sites
	-> Printing at chr: chrom1 pos:2208437 chunknumber 8000 contains 253 sites
	-> Printing at chr: chrom1 pos:2235388 chunknumber 8100 contains 265 sites
	-> Printing at chr: chrom1 pos:2260935 chunknumber 8200 contains 251 sites
	-> Printing at chr: chrom1 pos:2290717 chunknumber 8300 contains 256 sites
	-> Printing at chr: chrom1 pos:2322825 chunknumber 8400 contains 294 sites
	-> Printing at chr: chrom1 pos:2353516 chunknumber 8500 contains 251 sites
	-> Printing at chr: chrom1 pos:2380136 chunknumber 8600 contains 266 sites
	-> Printing at chr: chrom1 pos:2406105 chunknumber 8700 contains 251 sites
	-> Printing at chr: chrom1 pos:2433742 chunknumber 8800 contains 253 sites
	-> Printing at chr: chrom1 pos:2471725 chunknumber 8900 contains 251 sites
	-> Printing at chr: chrom1 pos:2497311 chunknumber 9000 contains 252 sites
	-> Printing at chr: chrom1 pos:2522795 chunknumber 9100 contains 265 sites
	-> Printing at chr: chrom1 pos:2549020 chunknumber 9200 contains 256 sites
	-> Printing at chr: chrom1 pos:2583621 chunknumber 9300 contains 425 sites
	-> Printing at chr: chrom1 pos:2644369 chunknumber 9400 contains 1009 sites
	-> Printing at chr: chrom1 pos:2678697 chunknumber 9500 contains 252 sites
	-> Printing at chr: chrom1 pos:2704161 chunknumber 9600 contains 251 sites
	-> Printing at chr: chrom1 pos:2730056 chunknumber 9700 contains 253 sites

	-> Allocated ~ 80 million nodes to the nodepool, this is not an estimate of the memory usage

	-> Allocated ~ 90 million nodes to the nodepool, this is not an estimate of the memory usage

	-> Allocated ~ 100 million nodes to the nodepool, this is not an estimate of the memory usage

	-> Allocated ~ 110 million nodes to the nodepool, this is not an estimate of the memory usage

	-> Allocated ~ 120 million nodes to the nodepool, this is not an estimate of the memory usage

	-> Allocated ~ 130 million nodes to the nodepool, this is not an estimate of the memory usage
	-> Printing at chr: chrom1 pos:2755874 chunknumber 9800 contains 252 sites
	-> Printing at chr: chrom1 pos:2793491 chunknumber 9900 contains 252 sites
	-> Printing at chr: chrom1 pos:2854440 chunknumber 10000 contains 253 sites
	-> Printing at chr: chrom1 pos:2900283 chunknumber 10100 contains 251 sites
	-> Printing at chr: chrom1 pos:2925806 chunknumber 10200 contains 255 sites

	-> Done reading data waiting for calculations to finish
	-> Done waiting for threads
	-> Output filenames:
		->"angsd/angsd_LC_GL2_maf0018_LDpruned_chrom1.arg"
		->"angsd/angsd_LC_GL2_maf0018_LDpruned_chrom1.beagle.gz"
		->"angsd/angsd_LC_GL2_maf0018_LDpruned_chrom1.mafs.gz"
	-> Thu Jul  8 11:17:36 2021
	-> Arguments and parameters for all analysis are located in .arg file
	-> Total number of sites analyzed: 2948168
	-> Number of sites retained after filtering: 0 
	[ALL done] cpu-time used =  670.35 sec
	[ALL done] walltime used =  675.00 sec
  1. log output, using angsd version: angsd version: 0.921 (htslib: 1.6) build(Jun 3 2019 10:11:40), same output for
    angsd version: 0.921 (htslib: 1.9) build(Aug 6 2018 13:54:50)
	-> angsd version: 0.921 (htslib: 1.6) build(Jun  3 2019 10:11:40)
	-> [prep_sites.cpp] Reading binary representation of 'list/LDpruned_snps_chrom1.list'
	-> [prep_sites.cpp] nChr: 1 loaded from binary filter file
	-> Filterfile contains major/minor information
	-> [abcFilter.cpp] -sites is still beta, use at own risk...
	-> Reading fasta: reference.fasta
	-> Parsing 55 number of samples 
	-> Region lookup 1/1

	-> Allocated ~ 10 million nodes to the nodepool, this is not an estimate of the memory usage
	-> Printing at chr: chrom1 pos:26605 chunknumber 100 contains 251 sites
	-> Printing at chr: chrom1 pos:54087 chunknumber 200 contains 536 sites

	-> Allocated ~ 20 million nodes to the nodepool, this is not an estimate of the memory usage
	-> Printing at chr: chrom1 pos:83464 chunknumber 300 contains 251 sites

	-> Allocated ~ 30 million nodes to the nodepool, this is not an estimate of the memory usage

	-> Allocated ~ 40 million nodes to the nodepool, this is not an estimate of the memory usage

	-> Allocated ~ 50 million nodes to the nodepool, this is not an estimate of the memory usage

	-> Allocated ~ 60 million nodes to the nodepool, this is not an estimate of the memory usage

	-> Allocated ~ 70 million nodes to the nodepool, this is not an estimate of the memory usage
	-> Printing at chr: chrom1 pos:125739 chunknumber 400 contains 322 sites
	-> Printing at chr: chrom1 pos:159057 chunknumber 500 contains 261 sites
	-> Printing at chr: chrom1 pos:185071 chunknumber 600 contains 252 sites
	-> Printing at chr: chrom1 pos:210603 chunknumber 700 contains 266 sites
	-> Printing at chr: chrom1 pos:235998 chunknumber 800 contains 252 sites
	-> Printing at chr: chrom1 pos:261687 chunknumber 900 contains 252 sites
	-> Printing at chr: chrom1 pos:287788 chunknumber 1000 contains 255 sites
	-> Printing at chr: chrom1 pos:313237 chunknumber 1100 contains 255 sites
	-> Printing at chr: chrom1 pos:341463 chunknumber 1200 contains 251 sites
	-> Printing at chr: chrom1 pos:367023 chunknumber 1300 contains 265 sites
	-> Printing at chr: chrom1 pos:392993 chunknumber 1400 contains 251 sites
	-> Printing at chr: chrom1 pos:421985 chunknumber 1500 contains 255 sites
	-> Printing at chr: chrom1 pos:447407 chunknumber 1600 contains 251 sites
	-> Printing at chr: chrom1 pos:473372 chunknumber 1700 contains 254 sites
	-> Printing at chr: chrom1 pos:499139 chunknumber 1800 contains 252 sites
	-> Printing at chr: chrom1 pos:524574 chunknumber 1900 contains 272 sites
	-> Printing at chr: chrom1 pos:550791 chunknumber 2000 contains 251 sites
	-> Printing at chr: chrom1 pos:576997 chunknumber 2100 contains 251 sites
	-> Printing at chr: chrom1 pos:602613 chunknumber 2200 contains 256 sites
	-> Printing at chr: chrom1 pos:628188 chunknumber 2300 contains 252 sites
	-> Printing at chr: chrom1 pos:654714 chunknumber 2400 contains 256 sites
	-> Printing at chr: chrom1 pos:680273 chunknumber 2500 contains 252 sites
	-> Printing at chr: chrom1 pos:705826 chunknumber 2600 contains 251 sites
	-> Printing at chr: chrom1 pos:731715 chunknumber 2700 contains 252 sites
	-> Printing at chr: chrom1 pos:757188 chunknumber 2800 contains 255 sites
	-> Printing at chr: chrom1 pos:782836 chunknumber 2900 contains 252 sites
	-> Printing at chr: chrom1 pos:808468 chunknumber 3000 contains 251 sites
	-> Printing at chr: chrom1 pos:835340 chunknumber 3100 contains 256 sites
	-> Printing at chr: chrom1 pos:860744 chunknumber 3200 contains 259 sites
	-> Printing at chr: chrom1 pos:886811 chunknumber 3300 contains 251 sites
	-> Printing at chr: chrom1 pos:912573 chunknumber 3400 contains 259 sites
	-> Printing at chr: chrom1 pos:938142 chunknumber 3500 contains 262 sites
	-> Printing at chr: chrom1 pos:968970 chunknumber 3600 contains 254 sites
	-> Printing at chr: chrom1 pos:997235 chunknumber 3700 contains 441 sites
	-> Printing at chr: chrom1 pos:1024752 chunknumber 3800 contains 252 sites
	-> Printing at chr: chrom1 pos:1052940 chunknumber 3900 contains 252 sites
	-> Printing at chr: chrom1 pos:1091770 chunknumber 4000 contains 251 sites
	-> Printing at chr: chrom1 pos:1117345 chunknumber 4100 contains 256 sites
	-> Printing at chr: chrom1 pos:1143084 chunknumber 4200 contains 252 sites
	-> Printing at chr: chrom1 pos:1168761 chunknumber 4300 contains 252 sites
	-> Printing at chr: chrom1 pos:1194498 chunknumber 4400 contains 253 sites
	-> Printing at chr: chrom1 pos:1219894 chunknumber 4500 contains 254 sites
	-> Printing at chr: chrom1 pos:1245388 chunknumber 4600 contains 253 sites
	-> Printing at chr: chrom1 pos:1270824 chunknumber 4700 contains 251 sites
	-> Printing at chr: chrom1 pos:1296372 chunknumber 4800 contains 252 sites
	-> Printing at chr: chrom1 pos:1321719 chunknumber 4900 contains 253 sites
	-> Printing at chr: chrom1 pos:1347777 chunknumber 5000 contains 251 sites
	-> Printing at chr: chrom1 pos:1373438 chunknumber 5100 contains 256 sites
	-> Printing at chr: chrom1 pos:1398893 chunknumber 5200 contains 253 sites
	-> Printing at chr: chrom1 pos:1433295 chunknumber 5300 contains 266 sites
	-> Printing at chr: chrom1 pos:1461135 chunknumber 5400 contains 252 sites
	-> Printing at chr: chrom1 pos:1488105 chunknumber 5500 contains 251 sites
	-> Printing at chr: chrom1 pos:1513731 chunknumber 5600 contains 254 sites
	-> Printing at chr: chrom1 pos:1539407 chunknumber 5700 contains 255 sites
	-> Printing at chr: chrom1 pos:1565194 chunknumber 5800 contains 253 sites
	-> Printing at chr: chrom1 pos:1591515 chunknumber 5900 contains 252 sites
	-> Printing at chr: chrom1 pos:1617466 chunknumber 6000 contains 264 sites
	-> Printing at chr: chrom1 pos:1642919 chunknumber 6100 contains 252 sites
	-> Printing at chr: chrom1 pos:1668362 chunknumber 6200 contains 255 sites
	-> Printing at chr: chrom1 pos:1697488 chunknumber 6300 contains 360 sites
	-> Printing at chr: chrom1 pos:1725824 chunknumber 6400 contains 252 sites
	-> Printing at chr: chrom1 pos:1751404 chunknumber 6500 contains 256 sites
	-> Printing at chr: chrom1 pos:1776875 chunknumber 6600 contains 285 sites
	-> Printing at chr: chrom1 pos:1822075 chunknumber 6700 contains 286 sites
	-> Printing at chr: chrom1 pos:1847550 chunknumber 6800 contains 253 sites
	-> Printing at chr: chrom1 pos:1875196 chunknumber 6900 contains 254 sites
	-> Printing at chr: chrom1 pos:1902184 chunknumber 7000 contains 514 sites
	-> Printing at chr: chrom1 pos:1947622 chunknumber 7100 contains 373 sites
	-> Printing at chr: chrom1 pos:1976072 chunknumber 7200 contains 252 sites
	-> Printing at chr: chrom1 pos:2002074 chunknumber 7300 contains 256 sites
	-> Printing at chr: chrom1 pos:2035738 chunknumber 7400 contains 254 sites
	-> Printing at chr: chrom1 pos:2063953 chunknumber 7500 contains 255 sites
	-> Printing at chr: chrom1 pos:2089757 chunknumber 7600 contains 251 sites
	-> Printing at chr: chrom1 pos:2115834 chunknumber 7700 contains 253 sites
	-> Printing at chr: chrom1 pos:2141217 chunknumber 7800 contains 251 sites
	-> Printing at chr: chrom1 pos:2167133 chunknumber 7900 contains 258 sites
	-> Printing at chr: chrom1 pos:2208437 chunknumber 8000 contains 253 sites
	-> Printing at chr: chrom1 pos:2235388 chunknumber 8100 contains 265 sites
	-> Printing at chr: chrom1 pos:2260935 chunknumber 8200 contains 251 sites
	-> Printing at chr: chrom1 pos:2290717 chunknumber 8300 contains 256 sites
	-> Printing at chr: chrom1 pos:2322825 chunknumber 8400 contains 294 sites
	-> Printing at chr: chrom1 pos:2353516 chunknumber 8500 contains 251 sites
	-> Printing at chr: chrom1 pos:2380136 chunknumber 8600 contains 266 sites
	-> Printing at chr: chrom1 pos:2406105 chunknumber 8700 contains 251 sites
	-> Printing at chr: chrom1 pos:2433742 chunknumber 8800 contains 253 sites
	-> Printing at chr: chrom1 pos:2471725 chunknumber 8900 contains 251 sites
	-> Printing at chr: chrom1 pos:2497311 chunknumber 9000 contains 252 sites
	-> Printing at chr: chrom1 pos:2522795 chunknumber 9100 contains 265 sites
	-> Printing at chr: chrom1 pos:2549020 chunknumber 9200 contains 256 sites
	-> Printing at chr: chrom1 pos:2583621 chunknumber 9300 contains 425 sites
	-> Printing at chr: chrom1 pos:2644369 chunknumber 9400 contains 1009 sites
	-> Printing at chr: chrom1 pos:2678697 chunknumber 9500 contains 252 sites
	-> Printing at chr: chrom1 pos:2704161 chunknumber 9600 contains 251 sites
	-> Printing at chr: chrom1 pos:2730056 chunknumber 9700 contains 253 sites

	-> Allocated ~ 80 million nodes to the nodepool, this is not an estimate of the memory usage

	-> Allocated ~ 90 million nodes to the nodepool, this is not an estimate of the memory usage

	-> Allocated ~ 100 million nodes to the nodepool, this is not an estimate of the memory usage

	-> Allocated ~ 110 million nodes to the nodepool, this is not an estimate of the memory usage

	-> Allocated ~ 120 million nodes to the nodepool, this is not an estimate of the memory usage
	-> Printing at chr: chrom1 pos:2755874 chunknumber 9800 contains 252 sites
	-> Printing at chr: chrom1 pos:2793491 chunknumber 9900 contains 252 sites
	-> Printing at chr: chrom1 pos:2854440 chunknumber 10000 contains 253 sites
	-> Printing at chr: chrom1 pos:2900283 chunknumber 10100 contains 251 sites
	-> Printing at chr: chrom1 pos:2925806 chunknumber 10200 contains 255 sites

	-> Done reading data waiting for calculations to finish
	-> Done waiting for threads
	-> Output filenames:
		->"angsd/angsd_LC_GL2_maf0018_LDpruned_chrom1.arg"
		->"angsd/angsd_LC_GL2_maf0018_LDpruned_chrom1.beagle.gz"
		->"angsd/angsd_LC_GL2_maf0018_LDpruned_chrom1.mafs.gz"
	-> Thu Jul  8 12:44:55 2021
	-> Arguments and parameters for all analysis are located in .arg file
	[ALL done] cpu-time used =  853.84 sec
	[ALL done] walltime used =  860.00 sec

My SNP list

head list/LDpruned_snps_chrom1.list

chrom1	1057	T	A
chrom1	2519	G	T
chrom1	2778	T	C
chrom1	3046	A	T
chrom1	3053	A	G
chrom1	3054	A	T
chrom1	3066	G	A
chrom1	3225	C	A
chrom1	3229	T	G
chrom1	3240	G	A

My scaffolds for which I have sites I want to analyse (in this case only one, i.e. scaffold "chrom1")

cut -f1 {input} | sort | uniq > list/LDpruned_Chrom_chrom1.list
head  list/LDpruned_Chrom_chrom1.list

chrom1

@sagitaninta
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Hi @tholtzem, thank you very much for coming here with this solution as it works well with version 0.921 indeed (got it installed with conda). So this problem is fixed on my side and I'll close this. I hope the latest version of angsd will be as stable soon.

This was referenced Oct 7, 2022
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isinaltinkaya added a commit that referenced this issue Oct 11, 2022
@isinaltinkaya
[fix]: Replace assert statements with aio assert
497af8f 
Add function aio::doAssert to replace asserts
Did not use aio::assert as name  since aio.h
namespace complains due to assert being a macro
Fixes the major bug explained in #527
Fixes issues #520 #474 #466 #420 #405 #396 #385
Possibly others; other issues should rerun the
commands using the latest version.
This was referenced Oct 11, 2022
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Merged
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[fix]: Fix assert bug related to DNDEBUG flags #527 ANGSD/angsd
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@sagitaninta @tholtzem